Is there a way to search a database of SAM HMMs with another HMM?
We have not yet had much success with our attempts to score HMMs against HMMs, though we have not, of course, tried all possible algorithms. Our best method so far is to combine the results of scoring all template sequences against a target HMM and the target sequence against all template HMMs. There is probably a better method, and some people have had success with profile-profile alignment, but (so far) it has not worked well in our hands. • Can I obtain a copy of the SAM software for use on local use on my computer? Yes, we encourage you to download a copy of the SAM software. It’s available free for academic use at the SAM web site. You may find additional functionality you need with the full SAM package that is not currently accessible through our web site. • Is SAM-T05 suitable for prediction of transmembrane domains? SAM-T99 and SAM-T02 have not been optimized for transmembrane predictions. They are “ok” on transmembrane predictions, but not nearly as good as tools optimized for
We have not yet had much success with our attempts to score HMMs against HMMs, though we have not, of course, tried all possible algorithms. Our best method so far is to combine the results of scoring all template sequences against a target HMM and the target sequence against all template HMMs. There is probably a better method, and some people have had success with profile-profile alignment, but (so far) it has not worked well in our hands. • Can I obtain a copy of the SAM software for use on local use on my computer? Yes, we encourage you to download a copy of the SAM software. It’s available free for academic use at the SAM web site. You may find additional functionality you need with the full SAM package that is not currently accessible through our web site. • Is SAM-T06 suitable for prediction of transmembrane domains? SAM-T99 and SAM-T02 have not been optimized for transmembrane predictions. They are “ok” on transmembrane predictions, but not nearly as good as tools optimized for
We have not yet had much success with our attempts to score HMMs against HMMs, though we have not, of course, tried all possible algorithms. Our best method so far is to combine the results of scoring all template sequences against a target HMM and the target sequence against all template HMMs. There is probably a better method, and some people have had success with profile-profile alignment, but (so far) it has not worked well in our hands. • Can I obtain a copy of the SAM software for use on local use on my computer? Yes, we encourage you to download a copy of the SAM software. It’s available free for academic use at the SAM web site. You may find additional functionality you need with the full SAM package that is not currently accessible through our web site. • Is SAM-T08 suitable for prediction of transmembrane domains? The iterated searches used in SAM-T08 (T2K, T04, and T06) have not been optimized for transmembrane predictions. They are “ok” on transmembrane predictions, but not
